X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fnj.Rd;h=3bd7f2fa4469d0581920388bbc6b5a01c08d0b73;hb=da67dccb93d35408baa48b141fcda921772c8b9c;hp=612d78038f435d3dee0a85679fdb9f25a7cbc161;hpb=bd55cf71ae1a3d20d237d7fdd36af138c21769df;p=ape.git

diff --git a/man/nj.Rd b/man/nj.Rd
index 612d780..3bd7f2f 100644
--- a/man/nj.Rd
+++ b/man/nj.Rd
@@ -27,7 +27,7 @@ nj(X)
 \seealso{
   \code{\link{write.tree}}, \code{\link{read.tree}},
   \code{\link{dist.dna}}, \code{\link{bionj}},
-  \code{\link{fastme}}
+  \code{\link{fastme}}, \code{\link{njs}}
 }
 \examples{
 ### From Saitou and Nei (1987, Table 1):
@@ -35,9 +35,10 @@ x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
        10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
        5, 6, 10, 9, 13, 8)
 M <- matrix(0, 8, 8)
-M[row(M) > col(M)] <- x
-M[row(M) < col(M)] <- x
-rownames(M) <- colnames(M) <- 1:8
+M[lower.tri(M)] <- x
+M <- t(M)
+M[lower.tri(M)] <- x
+dimnames(M) <- list(1:8, 1:8)
 tr <- nj(M)
 plot(tr, "u")
 ### a less theoretical example